ソフトウェア | 名称 | バージョン | 分類 |
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HKL-2000 | | データ収集 | PHASER | | 位相決定 | PHENIX | (phenix.refine: 1.7.3_928)精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 3B6Y 解像度: 2→36.148 Å / SU ML: 0.26 / σ(F): 1.34 / 位相誤差: 24.3 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2343 | 2253 | 5.04 % |
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Rwork | 0.1999 | - | - |
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obs | 0.2016 | 44746 | 99.38 % |
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all | - | 31663 | - |
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溶媒の処理 | 減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 40.39 Å2 / ksol: 0.35 e/Å3 |
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原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -7.3539 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 11.8543 Å2 | -0 Å2 |
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3- | - | - | -4.5004 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2→36.148 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3123 | 814 | 0 | 327 | 4264 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.008 | 4097 | X-RAY DIFFRACTION | f_angle_d1.116 | 5675 | X-RAY DIFFRACTION | f_dihedral_angle_d22.079 | 1605 | X-RAY DIFFRACTION | f_chiral_restr0.077 | 627 | X-RAY DIFFRACTION | f_plane_restr0.004 | 579 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2-2.0457 | 0.3187 | 136 | 0.2577 | 2502 | X-RAY DIFFRACTION | 95 | 2.0457-2.0933 | 0.2635 | 149 | 0.2451 | 2634 | X-RAY DIFFRACTION | 100 | 2.0933-2.1457 | 0.3074 | 138 | 0.2254 | 2626 | X-RAY DIFFRACTION | 100 | 2.1457-2.2037 | 0.278 | 136 | 0.2203 | 2616 | X-RAY DIFFRACTION | 100 | 2.2037-2.2685 | 0.2906 | 128 | 0.2157 | 2659 | X-RAY DIFFRACTION | 100 | 2.2685-2.3417 | 0.2983 | 126 | 0.2191 | 2648 | X-RAY DIFFRACTION | 100 | 2.3417-2.4254 | 0.305 | 147 | 0.2237 | 2627 | X-RAY DIFFRACTION | 100 | 2.4254-2.5225 | 0.2342 | 140 | 0.2088 | 2660 | X-RAY DIFFRACTION | 100 | 2.5225-2.6372 | 0.2698 | 152 | 0.2077 | 2632 | X-RAY DIFFRACTION | 100 | 2.6372-2.7762 | 0.2733 | 137 | 0.2118 | 2633 | X-RAY DIFFRACTION | 100 | 2.7762-2.9501 | 0.261 | 145 | 0.2195 | 2692 | X-RAY DIFFRACTION | 100 | 2.9501-3.1778 | 0.2442 | 151 | 0.2206 | 2658 | X-RAY DIFFRACTION | 100 | 3.1778-3.4973 | 0.244 | 144 | 0.2037 | 2652 | X-RAY DIFFRACTION | 99 | 3.4973-4.0028 | 0.2217 | 150 | 0.1913 | 2702 | X-RAY DIFFRACTION | 100 | 4.0028-5.0409 | 0.1693 | 146 | 0.1541 | 2738 | X-RAY DIFFRACTION | 100 | 5.0409-36.1534 | 0.1891 | 128 | 0.1897 | 2814 | X-RAY DIFFRACTION | 98 |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 1.6332 | 2.7001 | -2.0785 | 8.2781 | -3.7193 | 7.5469 | -0.0421 | 0.2951 | -0.8277 | 0.1538 | 0.1859 | 0.3139 | 0.3936 | -1.3807 | -0.1004 | 0.2452 | -0.0861 | -0.0421 | 0.3735 | 0.0204 | 0.3784 | 24.5603 | 119.1686 | -18.6104 | 2 | 3.7458 | 2.1629 | -1.4737 | 5.4419 | -1.8983 | 5.1533 | -0.3323 | 0.0538 | -0.5287 | -0.0501 | 0.0216 | -0.0138 | 0.5371 | -0.2568 | 0.1871 | 0.248 | -0.0267 | 0.0805 | 0.1318 | -0.0692 | 0.346 | 29.5535 | 110.6375 | -6.2881 | 3 | 4.0974 | 0.7559 | -0.1899 | 5.2206 | -0.5798 | 3.9295 | -0.1455 | 0.1593 | -0.5167 | -0.1074 | 0.017 | -0.2447 | 0.1322 | 0.2988 | 0.0928 | 0.1694 | -0.0335 | 0.0704 | 0.1173 | -0.0349 | 0.2704 | 35.0472 | 115.7809 | -11.5178 | 4 | 3.7879 | -0.5762 | -2.1944 | 4.9386 | 1.4451 | 6.1951 | -0.0809 | 0.4626 | -0.7004 | -0.375 | 0.1306 | 0.0314 | 0.5597 | -0.1067 | -0.0215 | 0.2585 | -0.0586 | 0.0324 | 0.1282 | -0.0829 | 0.3651 | 30.5407 | 114.2366 | -16.1139 | 5 | 3.7729 | -3.6293 | -4.4455 | 5.5719 | 4.9214 | 7.4966 | -0.4077 | 0.4801 | -0.6463 | -0.4971 | 0.4726 | -0.784 | 0.1203 | 0.8371 | -0.182 | 0.2509 | -0.1809 | 0.2439 | 0.4723 | -0.1487 | 0.6147 | 47.9671 | 120.4155 | -16.3576 | 6 | 7.4628 | -0.8634 | -5.7925 | 0.9848 | 0.4728 | 5.5887 | 0.2169 | -0.6624 | 0.7928 | 0.08 | 0.0406 | -0.3771 | -0.6562 | 0.6725 | -0.2588 | 0.3476 | -0.1283 | 0.0035 | 0.1571 | -0.0458 | 0.2952 | 34.7933 | 130.2779 | 2.108 | 7 | 5.4676 | 1.7681 | -0.8167 | 3.4561 | 0.2294 | 4.3613 | 0.2263 | -0.6286 | -0.1603 | 0.5331 | -0.0494 | 0.0757 | -0.2297 | 0.1124 | -0.1605 | 0.2209 | 0.0249 | 0.0499 | 0.1747 | 0.0196 | 0.2048 | 22.3362 | 120.9199 | 10.0923 | 8 | 4.9941 | 1.7818 | 1.4428 | 2.1295 | 2.8366 | 4.9387 | 0.1546 | -0.5984 | -0.5487 | 0.3928 | 0.0147 | -0.3755 | 0.2965 | 0.2183 | -0.1132 | 0.1883 | 0.0015 | 0.0029 | 0.1852 | 0.0775 | 0.1792 | 24.4323 | 116.7917 | 11.3442 | 9 | 7.1402 | 0.1991 | 1.0145 | 6.3512 | 0.4401 | 6.8151 | -0.0347 | -0.2564 | -0.0006 | 0.1567 | 0.107 | 0.2365 | -0.3062 | -0.1572 | -0.0906 | 0.1619 | -0.0231 | 0.0592 | 0.1171 | 0.0345 | 0.1508 | 22.5028 | 120.9762 | 4.4305 | 10 | 7.0257 | 0.5753 | -0.015 | 4.759 | 1.8657 | 6.7451 | -0.1175 | -1.158 | 0.1384 | 0.628 | 0.2107 | 0.2214 | -0.0887 | -0.6778 | 0.001 | 0.2831 | 0.1271 | 0.0713 | 0.3853 | 0.0661 | 0.2957 | -24.2477 | 120.8783 | 44.7245 | 11 | 1.8425 | -2.8998 | 0.5585 | 6.4275 | 0.0737 | 7.0811 | 0.0161 | -0.2088 | -0.9028 | 0.0219 | 0.0754 | -0.4801 | 1.1115 | 0.5608 | -0.2665 | 0.354 | 0.0953 | 0.0528 | 0.2004 | 0.1125 | 0.5346 | -13.8101 | 107.5024 | 33.1024 | 12 | 6.5671 | -2.0689 | -1.779 | 3.2774 | 0.5632 | 4.7503 | 0.0231 | -0.4836 | -0.5734 | 0.1146 | 0.2116 | 0.3875 | 0.048 | -0.7008 | -0.125 | 0.1974 | 0.0367 | 0.0694 | 0.3469 | 0.1183 | 0.2806 | -26.2163 | 116.2922 | 38.9375 | 13 | 5.1499 | 0.2388 | -1.4164 | 2.2573 | -0.516 | 2.3924 | 0.0007 | -1.1164 | -0.4078 | 0.5403 | 0.2688 | 0.3524 | -0.1525 | -0.351 | -0.0704 | 0.2598 | 0.0896 | 0.0688 | 0.517 | 0.071 | 0.2536 | -25.8967 | 118.6592 | 45.107 | 14 | 3.1577 | 0.0593 | -1.6018 | 1.7911 | -0.5698 | 3.7389 | -0.1315 | -0.0743 | 0.3043 | 0.3222 | 0.2297 | 0.4206 | -0.3311 | -0.5425 | -0.2667 | 0.2406 | 0.115 | 0.0551 | 0.1924 | -0.0153 | 0.2697 | -25.3202 | 130.3281 | 25.8082 | 15 | 4.3242 | -2.4474 | -0.4001 | 3.7319 | 0.0587 | 2.2919 | 0.186 | 0.5251 | -0.2417 | -0.616 | -0.062 | -0.1217 | -0.1189 | 0.0003 | -0.0933 | 0.2253 | -0.0163 | 0.0311 | 0.1318 | -0.0833 | 0.2496 | -13.2864 | 122.5219 | 17.3761 | 16 | 6.7332 | -1.5167 | 1.5519 | 5.6513 | 2.6952 | 2.1026 | 0.5449 | 0.8631 | -1.629 | -0.4137 | 0.1812 | -0.4778 | 0.5161 | 0.667 | -0.7019 | 0.4473 | -0.0065 | 0.0143 | 0.3298 | -0.1806 | 0.7382 | -14.0772 | 111.445 | 16.0317 | 17 | 6.0844 | -0.2633 | 0.9231 | 4.8381 | -0.48 | 6.1927 | -0.0367 | 0.0318 | 0.0215 | -0.4504 | 0.0369 | -0.0437 | -0.0717 | 0.0907 | 0.0443 | 0.1393 | 0.0279 | 0.066 | 0.0006 | -0.0585 | 0.1785 | -13.7839 | 120.4923 | 22.6957 | 18 | 0.2969 | -0.0038 | -0.1589 | 0.1517 | -0.0569 | 1.1295 | 0.2802 | -0.1385 | 0.2028 | -0.0296 | 0.0863 | 0.0199 | 0.0608 | -0.1375 | 0.5852 | 0.1627 | 0.0522 | 0.0659 | 0.4958 | -0.1836 | -0.0452 | 4.9485 | 122.5848 | 14.3971 | 19 | 0.2391 | -0.0175 | 0.0137 | 0.1781 | 0.0932 | 0.0475 | 0.1025 | 0.1319 | 0.2163 | -0.0343 | 0.1484 | 0.0309 | 0.0589 | 0.1173 | 0.0931 | 0.2257 | -0.0383 | 0.0192 | 0.4895 | 0.0742 | 0.1094 | 4.6191 | 122.4272 | 13.9915 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resseq 49:61)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 62:82)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 83:121)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 122:135)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 136:145)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 146:163)7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 164:191)8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resseq 192:214)9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resseq 215:243)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 54:69)11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 70:82)12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 83:116)13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resseq 117:145)14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resseq 146:163)15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resseq 164:201)16 | X-RAY DIFFRACTION | 16 | chain 'B' and (resseq 202:214)17 | X-RAY DIFFRACTION | 17 | chain 'B' and (resseq 215:245)18 | X-RAY DIFFRACTION | 18 | chain 'C' and ( | | | | | | | | | | | | | | | | | |
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